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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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) 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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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) 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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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) 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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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) 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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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) 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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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) 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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ), 'gf_id' => 'HOM05D001575', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001575' ), 'data_identifier' => 'HOM05D001575', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001575', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '78' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.1385' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2813' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3113' => 'aag', 'Actinidia00808' => 'ach', 'Actinidia07092' => 'ach', 'Actinidia20084' => 'ach', 'Actinidia27677' => 'ach', 'Actinidia37268' => 'ach', 'Actinidia37273' => 'ach', 'Ah.15g096730' => 'amhyb', 'Aqoxy2G01901' => 'aox', 'Aqoxy2G01926' => 'aox', 'Aqoxy4G03110' => 'aox', 'Aqoxy6G00347' => 'aox', 'arahy.Tifrunner.gnm1.ann1.9248BJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6R1ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISP71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR686J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SI5P19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWV6LC' => 'arhy', 'ATR0594G033' => 'atr', 'ATR0594G168' => 'atr', 'ATR0594G232' => 'atr', 'ATR1136G008' => 'atr', 'Atru.chr3.3766' => 'acertr', 'Atru.chr3.3767' => 'acertr', 'Atru.chr3.3779_Atru.chr3.3780' => 'acertr', 'AUR62001857' => 'cqu', 'AUR62009651' => 'cqu', 'AUR62009652' => 'cqu', 'AUR62032023' => 'cqu', 'AUR62035970' => 'cqu', 'AUR62035973' => 'cqu', 'AUR62043970' => 'cqu', 'CAN.G1666.3' => 'can', 'CAN.G170.128' => 'can', 'CAN.G689.9' => 'can', 'CAN.G84.10' => 'can', 'CAN.G84.11' => 'can', 'CAN.G971.4' => 'can', 'CANSAT01G1095' => 'cansat', 'CANSAT54G0238' => 'cansat', 'CANSAT54G0558' => 'cansat', 'Ca_01829_v3' => 'car', 'Ca_03411_v3' => 'car', 'Ca_04518_v3' => 'car', 'Ca_22433_v3' => 'car', 'Ca_29794_v3' => 'car', 'Cc00_g26220' => 'ccan', 'Cc01_g12020' => 'ccan', 'Cc03_g12410' => 'ccan', 'Cc07_g18290' => 'ccan', 'Cfa011408' => 'cfa', 'Cfa011414' => 'cfa', 'Cfa011415' => 'cfa', 'Ciclev10003729m.g' => 'ccl', 'Ciclev10028881m.g' => 'ccl', 'Ciclev10030276m.g' => 'ccl', 'CiPaw.13G102600' => 'cil', 'CiPaw.14G074400' => 'cil', 'ClCG02G000560' => 'cla', 'ClCG03G001790' => 'cla', 'COL.COLO4_12942' => 'col', 'COL.COLO4_18405' => 'col', 'COL.COLO4_18412' => 'col', 'COL.COLO4_33830' => 'col', 'COL.COLO4_35709' => 'col', 'Cpa.g.sc139.16' => 'cpa', 'Cpa.g.sc139.6' => 'cpa', 'CsaV3_1G033780' => 'csa', 'CsaV3_2G018250' => 'csa', 'CsaV3_6G021940' => 'csa', 'CSS0002223' => 'camsi', 'CSS0014558' => 'camsi', 'CSS0026647' => 'camsi', 'CSS0029072' => 'camsi', 'CSS0030851' => 'camsi', 'CSS0035490' => 'camsi', 'CSS0036984' => 'camsi', 'CSS0046801' => 'camsi', 'CSS0048642' => 'camsi', 'DCAR_015579' => 'dca', 'DCAR_016742' => 'dca', 'DCAR_018862' => 'dca', 'DCAR_018863' => 'dca', 'DCAR_018864' => 'dca', 'Dinv06295' => 'din', 'Dinv06296' => 'din', 'Dinv06339' => 'din', 'Dinv24339' => 'din', 'Dinv32826' => 'din', 'Duzib147G1076' => 'dzi', 'Duzib150G0023' => 'dzi', 'Duzib168G0344' => 'dzi', 'Duzib168G0665' => 'dzi', 'Duzib170G0887' => 'dzi', 'Duzib187G0320' => 'dzi', 'ECA236G3342' => 'eca', 'ECA236G4150' => 'eca', 'ECA246G2599' => 'eca', 'ECA247G1583' => 'eca', 'ECA247G4126' => 'eca', 'EL10Ac7g15935' => 'bvu', 'Eucgr.B02432' => 'egr', 'Eucgr.B02439' => 'egr', 'Eucgr.I00216' => 'egr', 'Eucgr.J02105' => 'egr', 'Eucgr.J02106' => 'egr', 'FAN02G4593' => 'fan', 'FAN05G2642' => 'fan', 'FAN05G5317' => 'fan', 'FAN09G0728' => 'fan', 'FAN11G1142' => 'fan', 'FAN11G2260' => 'fan', 'FAN14G0636' => 'fan', 'FAN14G1451' => 'fan', 'FAN14G2276' => 'fan', 'FAN16G3042' => 'fan', 'FAN19G0354' => 'fan', 'FAN21G2208' => 'fan', 'FAN21G2273' => 'fan', 'FAN23G1841' => 'fan', 'FAN23G2179' => 'fan', 'FAN23G2408' => 'fan', 'FAN25G0182' => 'fan', 'FAN26G0876' => 'fan', 'FvH4_1g24210' => 'fve', 'FvH4_3g34301' => 'fve', 'FvH4_3g34320' => 'fve', 'FvH4_3g34450' => 'fve', 'FvH4_6g05690' => 'fve', 'FvH4_6g27980' => 'fve', 'Glyma.01G142400' => 'gma', 'Glyma.03G030500' => 'gma', 'Glyma.09G121000' => 'gma', 'Glyma.11G146899' => 'gma', 'Glyma.13G330800' => 'gma', 'Glyma.13G330900' => 'gma', 'Glyma.15G043300' => 'gma', 'Gohir.A03G036600' => 'ghi', 'Gohir.A03G036700' => 'ghi', 'Gohir.A03G040600' => 'ghi', 'Gohir.A03G044400' => 'ghi', 'Gohir.A07G094000' => 'ghi', 'Gohir.A10G156300' => 'ghi', 'Gohir.D03G122800' => 'ghi', 'Gohir.D03G127533' => 'ghi', 'Gohir.D03G129100' => 'ghi', 'Gohir.D03G131500' => 'ghi', 'Gohir.D03G131600' => 'ghi', 'Gohir.D07G098600' => 'ghi', 'Gohir.D10G109400' => 'ghi', 'Gorai.001G106000' => 'gra', 'Gorai.003G129600' => 'gra', 'Gorai.003G134100' => 'gra', 'Gorai.003G135700' => 'gra', 'Gorai.003G135800' => 'gra', 'Gorai.003G138400' => 'gra', 'Gorai.003G138500' => 'gra', 'Gorai.011G120000' => 'gra', 'GSVIVG01025078001' => 'vvi', 'HanXRQChr01g0014441' => 'han', 'HanXRQChr01g0014451' => 'han', 'HanXRQChr05g0133841' => 'han', 'HanXRQChr05g0133851' => 'han', 'HanXRQChr05g0133861' => 'han', 'HanXRQChr05g0133871' => 'han', 'HanXRQChr05g0133881' => 'han', 'HanXRQChr05g0133891' => 'han', 'HanXRQChr05g0133901' => 'han', 'HanXRQChr05g0159761' => 'han', 'HanXRQChr06g0176051' => 'han', 'HanXRQChr08g0230551' => 'han', 'HanXRQChr15g0469681' => 'han', 'Haze_23979' => 'cav', 'Haze_23989' => 'cav', 'Haze_23993' => 'cav', 'Haze_25212' => 'cav', 'Hma1.2p1_0035F.1_g021750' => 'hma', 'Hma1.2p1_0035F.1_g021770' => 'hma', 'Hma1.2p1_0035F.1_g021780' => 'hma', 'Hma1.2p1_0321F.1_g124090' => 'hma', 'HPP92_022005' => 'vpl', 'HPP92_024853' => 'vpl', 'HPP92_024854' => 'vpl', 'HPP92_026602' => 'vpl', 'HPP92_026603' => 'vpl', 'Lalb_Chr01g0011951' => 'lal', 'Lalb_Chr22g0350051' => 'lal', 'Lj1A178G40' => 'lonja', 'Lj1A178T42' => 'lonja', 'Lj1C178G13' => 'lonja', 'Lj1C178T14' => 'lonja', 'Lj1C178T6' => 'lonja', 'Lj1P163T6' => 'lonja', 'Lj1P163T8' => 'lonja', 'Lj1P164T11' => 'lonja', 'Lj1P170T4' => 'lonja', 'Lj1P179T34' => 'lonja', 'Lj3g0000874' => 'lja', 'Lj3g0018806' => 'lja', 'Lj4A844T65' => 'lonja', 'Lj4g0022769' => 'lja', 'Lsat_1_v5_gn_5_2381' => 'lsa', 'Lsat_1_v5_gn_8_78921' => 'lsa', 'Lsat_1_v5_gn_8_78981' => 'lsa', 'Lsat_1_v5_gn_8_79001' => 'lsa', 'Lsat_1_v5_gn_8_79061' => 'lsa', 'Lsat_1_v5_gn_8_79101' => 'lsa', 'Lsat_1_v5_gn_9_21421' => 'lsa', 'Manes.04G028500' => 'mes', 'Manes.11G137300' => 'mes', 'Manes.11G138000' => 'mes', 'Manes.12G154300' => 'mes', 'Mapoly0092s0054' => 'mpo', 'Mapoly0117s0050' => 'mpo', 'MBI06_g35963_MAGBIO' => 'mbi', 'MBI06_g41416_MAGBIO' => 'mbi', 'MBI14_g03109_MAGBIO' => 'mbi', 'MBI14_g03112_MAGBIO' => 'mbi', 'MBI14_g12523_MAGBIO' => 'mbi', 'MBI14_g30337_MAGBIO' => 'mbi', 'MBI14_g30338_MAGBIO' => 'mbi', 'MBI14_g35790_MAGBIO' => 'mbi', 'MBI14_g36016_MAGBIO' => 'mbi', 'MD02G1278700' => 'mdo', 'MD03G1105600' => 'mdo', 'MD07G1046800' => 'mdo', 'MD11G1118100' => 'mdo', 'MD11G1119200' => 'mdo', 'Medtr0002s0040' => 'mtr', 'Medtr0002s1060' => 'mtr', 'Medtr0062s0020' => 'mtr', 'Medtr0062s0040' => 'mtr', 'Medtr0062s0060' => 'mtr', 'Medtr0062s0090' => 'mtr', 'Medtr0062s0110' => 'mtr', 'Medtr0062s0130' => 'mtr', 'Medtr0062s0170' => 'mtr', 'Medtr0263s0020' => 'mtr', 'Medtr0443s0040' => 'mtr', 'Medtr1457s0010' => 'mtr', 'Medtr2g036240' => 'mtr', 'Medtr2g036260' => 'mtr', 'Medtr2g036290' => 'mtr', 'Medtr2g096030' => 'mtr', 'Medtr2g096040' => 'mtr', 'Medtr6g079630' => 'mtr', 'Medtr8g046730' => 'mtr', 'MELO3C020685.2' => 'cme', 'MELO3C023247.2' => 'cme', 'MELO3C025718.2' => 'cme', 'Migut.F01368' => 'egut', 'Migut.H00728' => 'egut', 'Migut.N02646' => 'egut', 'Migut.O00690' => 'egut', 'MSTRG.9026' => 'ama', 'Nitab4.5_0001885g0010' => 'nta', 'Nitab4.5_0002380g0030' => 'nta', 'Nitab4.5_0004839g0040' => 'nta', 'Nitab4.5_0007396g0020' => 'nta', 'Nitab4.5_0011331g0010' => 'nta', 'Nitab4.5_0012789g0020' => 'nta', 'Nn2g10566' => 'nnu', 'Nn2g10567' => 'nnu', 'Nn2g10568' => 'nnu', 'Nn2g12818' => 'nnu', 'Oeu033660.1' => 'oeu', 'Oeu040998.1' => 'oeu', 'Oeu041001.1' => 'oeu', 'Oeu041002.1' => 'oeu', 'Oeu062290.1' => 'oeu', 'Os10g0416100' => 'osa', 'Os10g0416500' => 'osa', 'Os10g0416800' => 'osa', 'Peaxi162Scf00411g00083' => 'pax', 'Peaxi162Scf00589g00225' => 'pax', 'Peaxi162Scf00616g00611' => 'pax', 'Peaxi162Scf00616g00612' => 'pax', 'Peaxi162Scf00836g00035' => 'pax', 'Peaxi162Scf00836g00039' => 'pax', 'Peaxi162Scf00836g00311' => 'pax', 'Peaxi162Scf03664g00001' => 'pax', 'PGR079G0004' => 'pgr', 'PGR102G0352' => 'pgr', 'PGR102G3093' => 'pgr', 'PGR119G0438' => 'pgr', 'PGR119G0926' => 'pgr', 'PGR119G1330' => 'pgr', 'PGR119G2235' => 'pgr', 'PGSC0003DMG400015523' => 'stu', 'PGSC0003DMG400025352' => 'stu', 'PGSC0003DMG400025353' => 'stu', 'PGSC0003DMG400028682' => 'stu', 'Phvul.009G240550' => 'pvu', 'Phvul.009G240600' => 'pvu', 'Phvul.011G069900' => 'pvu', 'Phvul.L002311' => 'pvu', 'Potri.001G341700' => 'ptr', 'Potri.005G059400' => 'ptr', 'Potri.012G102400' => 'ptr', 'Potri.015G100500' => 'ptr', 'Potri.015G100600' => 'ptr', 'Pp3c6_90' => 'ppa', 'Prupe.2G041800' => 'ppe', 'Prupe.4G164000' => 'ppe', 'Prupe.6G088400' => 'ppe', 'Prupe.6G089400' => 'ppe', 'Prupe.6G119700' => 'ppe', 'Psat0s1279g0040' => 'psa', 'Psat0s1279g0080' => 'psa', 'Psat0s3644g0040' => 'psa', 'Psat0s3644g0080' => 'psa', 'Psat0s521g0080' => 'psa', 'Psat1g147000' => 'psa', 'Psat1g147560' => 'psa', 'Psat1g147600' => 'psa', 'Psat1g148600' => 'psa', 'Psat1g148720' => 'psa', 'Psat1g149040' => 'psa', 'Psat1g149080' => 'psa', 'Psat1g149120' => 'psa', 'Psat1g150480' => 'psa', 'Psat1g150520' => 'psa', 'Psat2g012080' => 'psa', 'Psat4g106120' => 'psa', 'Psat4g106160' => 'psa', 'Psat5g256760' => 'psa', 'Psat5g281960' => 'psa', 'PSO339G0548' => 'pso', 'PSO384G1386' => 'pso', 'PSO541G0760' => 'pso', 'PSO675G3569' => 'pso', 'QL01p034647' => 'qlo', 'QL01p034917' => 'qlo', 'QL06p028928' => 'qlo', 'QL06p028983' => 'qlo', 'RcHm_v2.0_Chr2g0120651' => 'rch', 'RcHm_v2.0_Chr3g0454591' => 'rch', 'RcHm_v2.0_Chr5g0061901' => 'rch', 'RcHm_v2.0_Chr5g0062101' => 'rch', 'RcHm_v2.0_Chr5g0062131' => 'rch', 'RcHm_v2.0_Chr5g0062171' => 'rch', 'Rhsim01G0223500' => 'rsi', 'Rhsim01G0223600' => 'rsi', 'SalBow3G2788' => 'sbo', 'SalBow3G4411' => 'sbo', 'Sc12g0001860' => 'sci', 'Sed0002554' => 'sed', 'Sed0014199' => 'sed', 'Sed0017394' => 'sed', 'SEGI_01261' => 'sgi', 'SEGI_01882' => 'sgi', 'SEGI_02884' => 'sgi', 'SEGI_04099' => 'sgi', 'SEGI_06979' => 'sgi', 'SEGI_08729' => 'sgi', 'SEGI_17569' => 'sgi', 'SEGI_22673' => 'sgi', 'SEGI_24422' => 'sgi', 'SEGI_26381' => 'sgi', 'SEGI_30512' => 'sgi', 'SEGI_30736' => 'sgi', 'SEGI_30871' => 'sgi', 'SEGI_36757' => 'sgi', 'SGA_v2.0_scaffold80G25733' => 'sas', 'SMO115G0212' => 'smo', 'SMO340G0242' => 'smo', 'Solyc11g005890.3' => 'sly', 'Solyc11g072750.3' => 'sly', 'Solyc11g072760.1' => 'sly', 'Solyc11g072830.1' => 'sly', 'Sopen11g030420' => 'spe', 'Sopen11g030430' => 'spe', 'Sopen11g030500' => 'spe', 'TAR623G1547' => 'tar', 'TAR623G1612' => 'tar', 'TAR633G1604' => 'tar', 'TAR633G2029' => 'tar', 'TAR633G2527' => 'tar', 'TAR633G2695' => 'tar', 'Thecc.01G129800' => 'tca', 'Thecc.09G331800' => 'tca', 'Thecc.09G331900' => 'tca', 'Thecc.09G332300' => 'tca', 'Thecc.09G332600' => 'tca', 'Thecc.09G333500' => 'tca', 'Thecc.09G333800' => 'tca', 'TPR.G11494' => 'tpr', 'TPR.G11526' => 'tpr', 'TPR.G19648' => 'tpr', 'TPR.G40314' => 'tpr', 'TPR.G40315' => 'tpr', 'TWI31G0821' => 'twi', 'TWI75G0235' => 'twi', 'TWI75G0259' => 'twi', 'TWI75G1203' => 'twi', 'TWI79G0128' => 'twi', 'TWI79G0403' => 'twi', 'VMungo0464G0842' => 'vmu', 'VMungo1080G1506' => 'vmu', 'VMungo1127G1299' => 'vmu', 'VMungo1309G1613' => 'vmu', 'Zm00001eb047940' => 'zma', 'Zm00001eb168350' => 'zma', 'Zm00001eb250900' => 'zma' ) $gf_id = 'HOM05D001575' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001575' ) $data_identifier = 'HOM05D001575' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aox' => (int) 4, 'arhy' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 2, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 1, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 6, 'gma' => (int) 7, 'ghi' => (int) 13, 'gra' => (int) 8, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 2, 'lonja' => (int) 11, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 19, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 20, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 3, 'sgi' => (int) 14, 'sas' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 3, 'tar' => (int) 6, 'tca' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb250900' $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